The Agent

Did the C.I.A. stop an F.B.I. detective from preventing 9/11?

Ali Soufan, as the F.B.I.’s lead investigator on the U.S.S. Cole bombing, suspected a larger Al Qaeda plot.

Illustration by Steve Brodner

On October 12, 2000, in the deep-water port of Aden, Yemen, the U.S.S. Cole, a guided-missile destroyer weighing eighty-three hundred tons, was docked at a fuelling buoy. The Cole, which cost a billion dollars to build, was one of the most “survivable” ships in the U.S. Navy, with seventy tons of armor, a hull that could withstand an explosion of fifty-one thousand pounds per square inch, and stealth technology designed to make the ship less visible to radar. As the Cole filled its tank, a fibreglass fishing boat containing plastic explosives approached. Two men brought the skiff to a halt amidships, smiled and waved, then stood at attention. The symbolism of this moment was exactly what Osama bin Laden, the leader of Al Qaeda, had hoped for when he approved a plan to attack an American naval vessel. “The destroyer represented the West,” bin Laden said later. “The small boat represented Muhammad.”

The shock wave from the blast shattered windows onshore. Two miles away, people thought there had been an earthquake. The fireball that rose from the waterline swallowed a sailor who had leaned over the rail to see what the men in the skiff were up to. The blast opened a hole, forty feet by forty feet, in the port side of the ship, tearing apart sailors belowdecks who were waiting for lunch. Seventeen of them perished, and thirty-nine were wounded. Several sailors swam through the blast hole to escape the flames. The great man-of-war looked like a gutted animal.

It was Al Qaeda’s second successful strike against American targets. In August, 1998, operatives had bombed the United States Embassies in Kenya and Tanzania simultaneously, killing two hundred and twenty-four people. Yet an important part of the Cole plot had failed: Fahd al-Quso, a member of Al Qaeda’s support team in Aden, was supposed to videotape the blast for propaganda purposes, but he slept through a morning alarm and did not set up his camera in time. Quso was in a taxi at the moment of the explosion, and he immediately went into hiding.

Shortly after the attack, Ali Soufan, a twenty-nine-year-old Lebanese-American, was driving across the Brooklyn Bridge when he received a page from the New York office of the F.B.I., where he was employed as a special agent. He was told to report to work at once. At the time, Soufan was the only F.B.I. agent in the city who spoke Arabic, and one of only eight in the country. He had joined the New York office in the fall of 1997, and his talents were quickly spotted by John O’Neill, the head of the F.B.I.’s National Security Division, which is devoted to combatting terrorism. The following February, when bin Laden issued a fatwa declaring war on America, Soufan wrote a trenchant report on Islamic fundamentalism that O’Neill distributed to his supervisors. After the 1998 embassy bombings, Soufan helped assemble the initial evidence linking them to bin Laden. Soufan’s language skills, his relentlessness, and his roots in the Middle East made him invaluable in helping the F.B.I. understand Al Qaeda, an organization that few Americans were even aware of before the embassy bombings. O’Neill, who had joined the F.B.I. twenty-five years earlier, referred to the young agent as a “national treasure.” Despite Soufan’s youth and his relatively short tenure, O’Neill placed him in charge of the Cole investigation. As it turned out, Soufan became America’s best chance to stop the attacks of September 11th.

Soufan speaks rapidly, and there is still a hint of Lebanon in his voice. He has an open face and an engaging smile, although there are circles under his eyes from too many long nights. Soufan is a Muslim, but he doesn’t follow any particular school of Islam; instead, he is drawn to mystical thought, especially that of Kahlil Gibran, the Lebanese-American poet. He told me that he has an interest in the Kabbalah, because “it appeared at a time when the political environment for the Jews was so harsh that they used this philosophy to escape their anguish.” When he wants to relax, he watches reruns of “Seinfeld”—he’s seen every episode three or four times—or Bugs Bunny cartoons. One of his favorite writers is Karen Armstrong, whose biographies of Muhammad and the Buddha knit together history and religion in a way that makes sense to him.

Soufan grew up in Lebanon during the calamitous civil war, when cities were destroyed and terrorists were empowered by lawlessness and chaos. His father was a journalist in Beirut, and as a child Soufan helped out at the business magazine his father produced, often carrying galleys to the printshop. In 1987, when Soufan was sixteen, the family moved to the United States. Soufan’s most vivid initial impression of his adopted country was that it was safe. “Also, it allowed me to dream,” he said.

Soufan lived in Pennsylvania, and he never suffered from prejudice because he was a Muslim Arab. In high school, he won many academic awards. He attended Mansfield University, in central Pennsylvania, where he was elected president of the student government. In 1997, he received a master’s degree in international relations from Villanova University, outside Philadelphia. He initially planned to continue his studies in a Ph.D. program. But he had developed a fascination with the U.S. Constitution—in particular, with its guarantees of freedom of speech, religion, and assembly, and the right to a speedy trial. “People who are born into this system may take it for granted,” he said. “You don’t know how important these rights are if you haven’t lived in a country where you can be arrested or killed and not even know why.” Like many naturalized citizens, Soufan felt indebted for the new life he had been given. Although he was poised for an academic career, he decided—“almost as a joke,” he says—to send his résumé to the F.B.I. He thought it was nearly inconceivable that the bureau would hire someone with his background. Yet in July, 1997, a letter arrived instructing him to report to the F.B.I. Academy, in Quantico, Virginia, in two weeks.

Upon graduation, Soufan went to the New York bureau. He was soon assigned to the I-40 squad, which concentrated mainly on the Islamist paramilitary group Hamas, but, in 1998, on the day after the East African embassy bombings, O’Neill drafted him into I-49, which had become the lead unit in the F.B.I.’s investigation of Al Qaeda.

O’Neill was one of a few top managers in the F.B.I. who recognized early the danger that Al Qaeda posed to America. His intensity was unyielding, and his manner was often abrasive; he could be brutal not only to those under him but to superiors who he felt were not fully committed to an investigation. Soufan proved to be a tireless ally, willing to work nights and holidays. “O’Neill adored him, and Ali felt the same way,” Carlos Fernandez, an agent who knew both men well, observed. “They were equals, in many ways. If you say something to Ali, he’ll remember it, word for word, ten years from now. John was also great at remembering names and connecting the dots. They could go on for hours, putting things together.” The fact that a novice like Soufan had direct access to O’Neill aroused some resentment among the other agents, but the bureau had nobody else with his skills and dedication. “John and I often talked about the need to clone Ali,” Kenneth Maxwell, an F.B.I. official who was then Soufan’s superior, told me.

The afternoon of the Cole bombing, Soufan and a few dozen other agents flew to Yemen to begin looking for evidence that could be used against Al Qaeda in court. (A larger contingent, which included O’Neill, was held up in Germany for a week, waiting for permission to enter the country.) Yemen was a particularly difficult place to start a terrorist investigation, as it was filled with active Al Qaeda cells and with sympathizers at very high levels of government. On television, Yemeni politicians called for jihad against America. When the agents landed in Aden, the day after the attack, Soufan looked out at a detachment of the Yemen Special Forces, who wore yellow uniforms with old Russian helmets; each soldier was aiming an AK-47 at the U.S. plane. A jittery, twelve-man hostage-rescue team, which had been sent along to protect the F.B.I. agents, responded by brandishing their M4s and handguns. Soufan realized that everyone might die on the tarmac if he didn’t do something quickly. He opened the plane’s door. One Yemeni soldier was holding a walkie-talkie. Soufan walked directly toward him, carrying a bottle of water as the guns followed him. It was a hundred and ten degrees outside.

“You look thirsty,” Soufan said, in Arabic, to the officer with the walkie-talkie. He handed him the bottle.

“Is it American water?” the officer asked.

Soufan assured him that it was, adding that he had American water for the other soldiers as well. The Yemenis considered the water such a precious commodity that some would not drink it. With this simple act of friendship, the soldiers lowered their weapons.

Soufan divided the agents on the ground into four teams. The first three were responsible for forensics, intelligence, and security; the last was devoted to exchanging information with Yemeni authorities. Just getting permission from the Yemeni government to go to the crime scene—the wounded warship in the Aden harbor—required lengthy negotiations with hostile officials. Security was a great concern, considering that automatic weapons were ubiquitous in the country, especially in rural areas, but Barbara Bodine, the American Ambassador, refused to allow the agents to carry heavy arms. She was concerned about offending the Yemeni authorities.

When Soufan and the investigators visited the ship, clumps of flesh were strewn belowdecks, amid the tangled mass of wire and metal. F.B.I. divers, hoping to make DNA identifications of the victims and the bombers, netted body parts floating in the waters around the ship. Looking through the huge blast hole, Soufan could see the mountainous, ancient city of Aden, rising above the curved harbor like a classical ampitheatre. He figured that, somewhere in the city, a camera had been set up to record the explosion, since terrorists regularly documented their work. Although the bombers were likely dead, a cameraman might still be at large.

When O’Neill finally arrived in Aden with the other agents, he was puzzled, upon getting off the plane, to see the Yemeni soldiers saluting. “I told them you were a general,” Soufan explained to him.

Yemen is a status-conscious society, and, because Soufan had promoted O’Neill to “general,” his counterpart was General Ghalib Qamish, the head of Yemeni intelligence. Every night, when the Yemeni authorities did business, Soufan and O’Neill spent hours pushing for access to witnesses, evidence, and crime scenes. Initially, the Yemenis told them that, since both of the bombers were dead, there was nothing to investigate. But who gave them money? Soufan asked. Who provided the explosives? The boat? He gently prodded the Yemenis to help him.

A few days after the bombing, the Yemenis brought in two known associates of bin Laden’s for questioning. One was named Jamal Badawi; the other was Fahd al-Quso, the man who had failed to videotape the Cole attack. Both men were Yemeni citizens. Quso, who ran a guesthouse in Aden for jihadis, had turned himself in after family members were questioned. He did not admit his role in the Cole plot, but he and Badawi confessed that they had recently travelled to Afghanistan, and had met there with a one-legged jihadi named Khallad. Badawi said that he had bought a boat for Khallad, who, he explained, had wanted to go into the fishing business. The Yemenis eventually determined that this was the boat used in the Cole bombing.

When Soufan heard that Quso had mentioned the name Khallad, he was startled: he had heard it from a source he had recruited a few years earlier, in Afghanistan. The source had told him that he had met a fighter in Kandahar with a metal leg who was one of bin Laden’s top lieutenants. When Soufan asked to speak to Quso and Badawi, the Yemenis told him that the men had sworn on a Koran that they were innocent of any crime. For them, that settled the matter.

Soufan and O’Neill knew that General Qamish represented their best hope of gaining any coöperation. He was a small, gaunt man whose face reminded Soufan of Gandhi’s. Despite the tensions between the two sides, Qamish had begun calling his American colleagues Brother John and Brother Ali. One night, O’Neill and Soufan spent many hours asking Qamish for passport photographs of suspected plotters, especially that of Khallad. He said repeatedly that the F.B.I. was not needed on the case, but O’Neill and Soufan pointed out that the sooner they could interrogate suspects linked to the Cole bombing the sooner they might obtain intelligence that could destroy Al Qaeda. The following night, Qamish announced, “I have your photos for you.” Soufan immediately sent Khallad’s photo to the C.I.A. He also faxed it to an F.B.I. agent in Islamabad, Pakistan; the agent showed it to Soufan’s source in Afghanistan, who identified the man as Khallad, the Al Qaeda lieutenant. This suggested strongly that Al Qaeda was behind the Cole attack.

Another break came that same evening, when a twelve-year-old boy named Hani went to the local police. He said that he had been fishing on a pier when the bombers placed their skiff in the water. One of the men had paid the boy a hundred Yemeni riyals—about sixty cents—to watch his Nissan truck and boat trailer, but he never returned. When the police heard Hani’s story, they locked him in jail and arrested his father as well.

After repeated requests, the Americans got permission to interview the boy and to examine the launch site. Hani was scared, but he provided a description of the bombers: one was heavy, and the other was “handsome.” An Arabic-speaking naval investigator named Robert McFadden offered the boy some candy. He then said that the bombers had invited him and his family to take a ride in the boat, which was white, with red carpeting on the floor. When Soufan heard this, he deduced that the bombers had been trying to determine how much weight the skiff could carry.

The abandoned truck and trailer were still at the launch site. It was a major mistake on the part of Al Qaeda not to have retrieved them. By checking registration records, investigators connected the truck and trailer to a house in a neighborhood of Aden called Burayqah. When Soufan went to the house, which was surrounded by a wall and a gate, he had an eerie feeling: this residence had a striking resemblance to the house in Nairobi where the bomb for the 1998 embassy attack had been made. Inside, in the master bedroom, there was a prayer rug oriented to the north, toward Mecca. The bathroom sink was full of body hair; the bombers had shaved and performed ritual ablutions before going to their deaths. Soufan’s men collected a razor and hair samples, which might provide the F.B.I. with the DNA evidence necessary to establish the identity of the killers. (So far, the investigators at the Cole site had found only a couple of bone fragments that didn’t belong to American sailors.)

Investigators found that another house in Aden had been rented by the terrorists; it was registered to “Abda Hussein Muhammad.” The name was dimly familiar to Soufan. At one point during the Nairobi investigation, a witness had mentioned an Al Qaeda operative named Nasheri who had proposed attacking an American vessel in Aden. Soufan did some research and discovered that Nasheri’s full name was Abdul Rahim Muhammad Hussein Abda al-Nasheri. The middle names were the same, just reversed. Soufan’s hunch paid off when American agents discovered a car in Aden that was registered to Nasheri. It was another strong link between Al Qaeda and the Cole attack.

A couple of weeks after the bombing, Yemeni authorities placed Badawi and Quso, the two Al Qaeda operatives, under arrest, apparently as a precaution. Soufan continued to press General Qamish to let him interrogate the men directly, and finally, after several weeks, Qamish relented.

Soufan spent hours preparing for the encounters, with the goal of finding some common ground with his subjects. Often, the bond centered on religion. “Ali was very spiritual,” Carlos Fernandez recalled. “In Yemen, he was reading the Koran at night. He would talk to these guys about their beliefs. Sometimes, he would actually convince them that their understanding of Islam was all wrong.”

In the interrogation of Badawi, Soufan learned that the skiff had been purchased in Saudi Arabia. Soufan questioned Quso over the course of several days. Quso was small, wiry, and insolent, with a wispy beard that he kept tugging on. Before Soufan could even begin, a local intelligence official came into the room and kissed Quso on both cheeks—a shocking signal that the security services were sympathetic to the jihadis. McFadden, who participated in the interrogations, recalled that Soufan was not intimidated. He said, “Ali was a natural interviewer, and he was able to dislodge Quso from his circle of comfort.” Eventually, Quso began to open up. He had been in Afghanistan, and boasted that he had fought beside bin Laden. He said that bin Laden had inspired him with his speeches about expelling the infidels from the Arabian peninsula—in particular, American troops stationed in Saudi Arabia.

Finally, Quso admitted that he was supposed to film the bombing but had overslept. (The Yemenis later found a video camera at his sister’s house.) He also said that several months before the Cole attack he and one of the bombers had delivered thirty-six thousand dollars to Khallad, the one-legged Al Qaeda lieutenant, in Bangkok. The money, Quso added, was meant only to buy Khallad a new prosthesis.

Soufan was suspicious of this explanation. Why had Al Qaeda sent money out of Yemen just before the Cole bombing took place? Money always flowed toward an operation, not away from it. He wondered if Al Qaeda had a bigger plot under way.

The C.I.A. had officials in Yemen to collect intelligence about Al Qaeda, and Soufan asked them if they knew anything about a new operation, perhaps in Southeast Asia. They professed to be as puzzled as he was. In November, 2000, a month after the Cole bombing, Soufan sent the agency the first of several official queries. On Soufan’s behalf, the director of the F.B.I. sent a letter to the director of the C.I.A., formally asking for information about Khallad, and whether there might have been an Al Qaeda meeting somewhere in Southeast Asia before the bombing. The agency said that it had nothing. Soufan trusted this response; he thought that he had a good working relationship with the agency.

Quso had told Soufan that when he and the Cole bomber went to Bangkok to meet Khallad they had stayed in the Washington Hotel. F.B.I. agents went through phone records to verify his story. They found calls between the hotel and Quso’s house, in Yemen. They also noticed that there were calls to both places from a pay phone in Kuala Lumpur, Malaysia. In April, 2001, Soufan sent another official teletype to the C.I.A., along with the passport photo of Khallad. He asked whether the telephone numbers had any significance, and whether there was any connection between the numbers and Khallad. The C.I.A. said that it could not help him.

In fact, the C.I.A. knew a lot about Khallad and his ties to Al Qaeda. The F.B.I. and the C.I.A. have long quarrelled over bureaucratic turf, and their mandates place them at odds. The ultimate goal of the bureau in gathering intelligence is to gain convictions for crimes; for the agency, intelligence itself is the object. If the agency had responded candidly to Soufan’s requests, it would have revealed its knowledge of an Al Qaeda cell that was already forming inside the United States. But the agency kept this intelligence to itself.

“I come from a generation of F.B.I. agents who have always worked closely with the C.I.A.,” Soufan told me. At the time he joined the bureau, law enforcement had become internationalized. In the nineteen-nineties, his mentor, O’Neill, had established close relations with foreign police services, an approach that sometimes encroached on the C.I.A.’s territory. In 1999, O’Neill sent Soufan and his supervisor, Pasquale D’Amuro, to Jordan, where authorities had discovered that jihadis linked to Al Qaeda were plotting to bomb tourist sites and hotels. Information that the Jordanians shared with Soufan made him realize that the intelligence that the C.I.A. was reporting was deeply flawed. His analysis forced local C.I.A. representatives to withdraw twelve cables that they had sent to agency headquarters. On the floor of the C.I.A.’s station in Amman, Soufan discovered a box of evidence that had been given to the agency by Jordanian intelligence. Such evidence is what the F.B.I. needs in order to mount prosecutions, and no one had examined the box’s contents or turned it over to the bureau. In the box, Soufan found a map of the proposed bomb sites, which proved crucial in the prosecutions of twenty-eight plotters in Jordan, twenty-two of whom were convicted. Soufan’s success embarrassed the C.I.A., deepening the rift between the two institutions. “The C.I.A. people couldn’t stand the fact that Ali’s opinion and analysis were correct,” an F.B.I. counterterrorism official who worked with Soufan told me. “He was an Arabic speaker and an F.B.I. agent on the ground who was running circles around them.”

Nevertheless, the C.I.A. recognized Soufan’s abilities and repeatedly tried to recruit him. “Come over to the Dark Side,” an agency operative once said to him. “You know you’re interested.” Soufan said that he just laughed.

Indeed, some of the C.I.A.’s best information about Al Qaeda came from the F.B.I. In 1998, F.B.I. investigators found an essential clue—a phone number in Yemen that functioned as a virtual switchboard for the terror network. The bombers in East Africa called that number before and after the attacks; so did Osama bin Laden. The number belonged to a jihadi named Ahmed al-Hada. By combing through the records of all the calls made to and from that number, F.B.I. investigators constructed a map of Al Qaeda’s global organization. The phone line was monitored as soon as it was discovered. But the C.I.A., as the primary organization for gathering foreign intelligence, had jurisdiction over conversations on the Hada phone, and did not provide the F.B.I. with the information it was getting about Al Qaeda’s plans.

A conversation on the Hada phone at the end of 1999 mentioned a forthcoming meeting of Al Qaeda operatives in Malaysia. The C.I.A. learned the name of one participant, Khaled al-Mihdhar, and the first name of another: Nawaf. Both men were Saudi citizens. The C.I.A. did not pass this intelligence to the F.B.I.

However, the C.I.A. did share the information with Saudi authorities, who told the agency that Mihdhar and a man named Nawaf al-Hazmi were members of Al Qaeda. Based on this intelligence, the C.I.A. broke into a hotel room in Dubai where Mihdhar was staying, en route to Malaysia. The operatives photocopied Mihdhar’s passport and faxed it to Alec Station, the C.I.A. unit devoted to tracking bin Laden. Inside the passport was the critical information that Mihdhar had a U.S. visa. The agency did not alert the F.B.I. or the State Department so that Mihdhar’s name could be put on a terror watch list, which would have prevented him from entering the U.S.

The C.I.A. asked Malaysian authorities to provide surveillance of the meeting in Kuala Lumpur, which took place on January 5, 2000, at a condominium overlooking a golf course designed by Jack Nicklaus. The condo was owned by a Malaysian businessman who had ties to Al Qaeda. The pay phone that Soufan had queried the agency about was directly in front of the condo. Khallad used it to place calls to Quso in Yemen. Although the C.I.A. later denied that it knew anything about the phone, the number was recorded in the Malaysians’ surveillance log, which was given to the agency.

At the time of the Kuala Lumpur meeting, Special Branch, the Malaysian secret service, photographed about a dozen Al Qaeda associates outside the condo and visiting nearby Internet cafés. These pictures were turned over to the C.I.A. The meeting was not wiretapped; had it been, the agency might have uncovered the plots that culminated in the bombing of the Cole and the September 11, 2001, attacks. On January 8th, Special Branch notified the C.I.A. that three of the men who had been at the meeting—Mihdhar, Hazmi, and Khallad—were travelling together to Bangkok. There Khallad met with Quso and one of the suicide bombers of the Cole. Quso gave Khallad the thirty-six thousand dollars, which was most likely used to buy tickets to Los Angeles for Mihdhar and Hazmi and provide them with living expenses in the U.S. Both men ended up on planes involved in the September 11th attacks.

In March, the C.I.A. learned that Hazmi had flown to Los Angeles two months earlier, on January 15th. Had the agency checked the flight manifest, it would have noticed that Mihdhar was travelling with him. Once again, the agency neglected to inform the F.B.I. or the State Department that at least one Al Qaeda operative was in the country.

Although the C.I.A. was legally bound to share this kind of information with the bureau, it was protective of sensitive intelligence. The agency sometimes feared that F.B.I. prosecutions resulting from such intelligence might compromise its relationships with foreign services, although there were safeguards to protect confidential information. The C.I.A. was particularly wary of O’Neill, who demanded control of any case that touched on an F.B.I. investigation. Many C.I.A. officials disliked him and feared that he could not be trusted with sensitive intelligence. “O’Neill was duplicitous,” Michael Scheuer, the official who founded Alec Station but has now left the C.I.A., told me. “He had no concerns outside of making the bureau look good.” Several of O’Neill’s subordinates suggested that the C.I.A. hid the information out of personal animosity. “They hated John,” the F.B.I. counterterrorism official assigned to Alec Station told me. “They knew that John would have marched in there and taken control of that case.”

The C.I.A. may also have been protecting an overseas operation and was afraid that the F.B.I. would expose it. Moreover, Mihdhar and Hazmi could have seemed like attractive recruitment possibilities—the C.I.A. was desperate for a source inside Al Qaeda, having failed to penetrate the inner circle or even to place someone in the training camps, even though they were largely open to anyone who showed up. However, once Mihdhar and Hazmi entered the United States they were the province of the F.B.I. The C.I.A. has no legal authority to operate inside the country.

In the end, the C.I.A.’s failure to inform the F.B.I. may be best explained by the fact that the agency was drowning in a flood of threats and warnings, and simply did not see the pivotal importance of this intelligence. Whatever the reason for the C.I.A.’s lapse, many F.B.I. investigators remain furious that they were not informed of the presence of Al Qaeda operatives inside America. Mihdhar and Hazmi arrived twenty months before September 11th. Kenneth Maxwell, Soufan’s former supervisor, told me, “Two Al Qaeda guys living in California—are you kidding me? We would have been on them like white on snow: physical surveillance, electronic surveillance, a special unit devoted entirely to them.” Of course, the F.B.I. had other opportunities to prevent September 11th. In July, 2001, an F.B.I. agent in Phoenix suggested interviewing Arabs enrolled in American flight schools; a month later, the bureau’s Minnesota office requested permission to aggressively investigate Zacarias Moussaoui, who later confessed to being an Al Qaeda associate. Both proposals were rejected by F.B.I. supervisors. But Mihdhar and Hazmi were directly involved in the September 11th conspiracy. Because of their connection to bin Laden, who had a federal indictment against him, the F.B.I. had all the authority it needed to use every investigative technique to penetrate and disrupt the Al Qaeda cell. Instead, the hijackers were free to develop their plot until it was too late to stop them.

In Yemen, the security situation deteriorated rapidly. Soufan and the other F.B.I. agents were quartered at the Aden Hotel, crammed in with other U.S. military and government employees, including Marine guards, and billeted three and four to a room; several dozen slept on bedrolls in the hotel ballroom. Gunfire erupted outside the hotel so frequently that the agents slept in their clothes, with their weapons at their sides. Agents learned from a mechanic in Aden that, after the bombing, some men brought to his shop a truck similar to the one used by the bombers; the men wanted to have metal plates installed in such a way that they could direct the force of an explosion. Certainly, the most tempting target for such a bomb would be the Aden Hotel. It wasn’t clear that the Yemeni government troops who were guarding the hotel with machine-gun nests would truly protect the Americans. “We were prisoners,” an agent recalled.

One night, shots were fired on the street while O’Neill was running a meeting inside the hotel. The marines and the hostage-rescue team adopted defensive positions. Soufan ventured out, unarmed, to talk to the Yemeni troops.

“Hey, Ali!” O’Neill called out. “Be careful!” He raced down the steps of the hotel to make sure Soufan was wearing his flak jacket. Frustration, stress, and danger, along with the enforced intimacy of their situation, had brought the two men even closer. O’Neill had begun to describe Soufan as his “secret weapon.” Speaking to the Yemenis, he called him simply “my son.”

Snipers covered Soufan as he approached a Yemeni officer, who assured him that everything was O.K.

“If everything is O.K., why are there no cars on the street?” Soufan asked.

The officer said that there must be a wedding nearby. Soufan looked around and saw that the hotel was surrounded by a large number of men in traditional dress—some in Jeeps, all carrying guns. They were civilians, not soldiers. They could be intelligence officers, or a tribal group bent on revenge. In either case, they easily outnumbered the Americans. Soufan was reminded of the 1993 uprising in Somalia, which ended with eighteen American soldiers dead, and one of the bodies being dragged through the streets of Mogadishu. The hotel backed up to the harbor, and the Americans were essentially trapped.

After Soufan went inside and offered his assessment of the situation, O’Neill ordered the marines to deploy two armored vehicles to block the street in front of the hotel. The night passed without further incident, but the next day O’Neill moved the investigators to the U.S.S. Duluth, stationed ten miles away, in the Bay of Aden. That proved to be a dangerous mistake. The next morning, when O’Neill and Soufan were flying back to town, their helicopter suddenly lurched into violent evasive maneuvers. The pilot reported that an SA-7 missile had locked in on them. O’Neill decided to send most of the investigators home; those who remained returned to the deserted hotel.

Just before Thanksgiving, the F.B.I. pulled O’Neill out of Yemen, apparently as a concession to Ambassador Bodine, who felt that the F.B.I. presence was straining diplomatic relations between America and Yemen. Soufan stayed on, but the threats in Aden became so acute that he and the other agents moved to the American Embassy in Sanaa, Yemen’s capital. The investigation was losing its momentum.

In the spring of 2001, Tom Wilshire, a C.I.A. liaison at F.B.I. headquarters, in Washington, was studying the relationship between Khaled al-Mihdhar, the Saudi Al Qaeda operative, and Khallad, the one-legged jihadi. Because of the similarity of the names, the C.I.A. had thought that they might be the same person, but, thanks in part to Ali Soufan’s investigations in Yemen, the agency now knew that they were not, and that Khallad had orchestrated the Cole attack. “O.K. This is important,” Wilshire said of Khallad, in an e-mail to his supervisors at the C.I.A. Counterterrorist Center. “This is a major-league killer.” Wilshire already knew that Hazmi, the other Saudi operative, had arrived in the United States and that Mihdhar was possibly with him. “Something bad [is] definitely up,” Wilshire wrote to a colleague. He asked permission to disclose this vital information to the F.B.I. His superiors at the C.I.A. never responded to his request. (In an official statement, the C.I.A. questioned the accuracy of this article but did not address specific allegations. It said, “Based on rigorous internal and external reviews of its shortcomings and successes before and after 9/11, the C.I.A. has improved its processing and sharing of intelligence. C.I.A.’s focus is on learning and even closer coöperation with partners inside and outside government, not on public finger pointing, which does not serve the American people well.”)

That summer, Wilshire asked an F.B.I. analyst to review the material on the Malaysia meeting, but he did not reveal that some of the participants might be in the United States. More important, he conveyed none of the urgency reflected in his e-mail; he told the analyst that she should examine the material in her free time. She didn’t get around to it until the end of July.

Wilshire did want to know, however, what the F.B.I. knew. He asked Dina Corsi, another F.B.I. analyst, to show three surveillance photos from the Malaysia meeting to several I-49 agents. The pictures showed Mihdhar and Hazmi and a man who, the C.I.A. believed, resembled Quso, the Cole cameraman. Wilshire told Corsi that one of the men was named Khaled al-Mihdhar, but he did not explain why the pictures had been taken, and he did not mention that Mihdhar had a U.S. visa.

According to the 9/11 Commission Report, on June 11th a C.I.A. supervisor went with the F.B.I. analyst and Corsi to New York to meet with F.B.I. case agents on the Cole investigation; Soufan, who was still in Yemen, did not attend. The meeting started in mid-morning, with the New York agents briefing the C.I.A. supervisor, Clark Shannon, for three or four hours on the progress of their investigation. Corsi then showed the three Malaysia photographs to her F.B.I. colleagues. They were high-quality surveillance photos. One, shot from a low angle, showed Mihdhar and Hazmi standing beside a tree in Malaysia. Shannon wanted to know if the agents recognized anyone. The I-49 agents asked who was in the pictures, and when and where they had been taken. “Were there any other photographs of this meeting?” one of the F.B.I. agents demanded. Shannon refused to say. Corsi promised that “in the days and weeks to come” she would try to get permission to pass that information along. The meeting became heated. The F.B.I. agents sensed that these photographs pertained directly to crimes they were trying to solve, but they couldn’t elicit any further information from Shannon. Corsi finally dropped the name Khaled al-Mihdhar. Steve Bongardt, Soufan’s top assistant in the Cole investigation, asked Shannon to provide a date of birth or a passport number to go with Mihdhar’s name. A name by itself was not sufficient to prevent his entry into the United States. Bongardt had just returned from Pakistan with a list of thirty names of suspected Al Qaeda associates and their dates of birth, which he had given to the State Department. That was standard procedure—the first thing most investigators would do. But Shannon declined to provide the additional information. Top C.I.A. officials had not authorized him to disclose the vital details of Mihdhar’s U.S. visa, his association with Hazmi, and their affiliation with Khallad and Al Qaeda.

There was a fourth photograph of the Malaysia meeting that Shannon did not produce. That was a picture of Khallad, the one-legged operative. Thanks to Soufan’s interrogation of Quso, the Cole investigators had an active file on Khallad and were preparing to indict him. Knowledge of that fourth photo would likely have prompted O’Neill to demand that the C.I.A. turn over all information relating to Khallad and his associates. By withholding the picture of Khallad attending the meeting with the future hijackers, the C.I.A. may in effect have allowed the September 11th plot to proceed. That summer, Mihdhar returned to Yemen and then went to Saudi Arabia, where, presumably, he helped the remaining hijackers secure entry into the United States. Two days after the frustrating June 11th meeting, Mihdhar received another American visa from the consulate in Jeddah, Saudi Arabia. Since the C.I.A. had not given his name to the State Department to post on its watch list, Mihdhar arrived in New York on the Fourth of July.

The June 11th meeting was the culmination of a strange trend in the U.S. government toward hiding information from the people who most needed it. In this regard, the F.B.I. was as guilty as the C.I.A. A federal law at the time prohibited the sharing of information arising from grand-jury testimony, but the F.B.I. took it as a nearly absolute bar to revealing any investigative evidence and, as a result, repeatedly turned down requests for information from other intelligence agencies. (The Joint Congressional Inquiry on 9/11 claimed that the law “came to be used simply as an excuse for not sharing information.”)

In 1995, the Justice Department established a policy, known as “the Wall,” which regulated the exchange of foreign intelligence information between agents and criminal investigators. Managers at F.B.I. headquarters misinterpreted the policy, turning it into a straitjacket for their own investigators. Intelligence agents were warned that sharing such information with criminal agents could mean the end of their careers. The Wall, the F.B.I. decided, separated even people who were on the same squad. The F.B.I. also began withholding intelligence from the White House. Every morning on the classified computers of the National Security Council, there were at least a hundred reports, from the C.I.A., the N.S.A., and other intelligence branches, but the F.B.I. never disseminated information.

The C.I.A. embraced the idea of the Wall with equal vigor. The agency frequently decided not to share intelligence with the F.B.I. on the ground that it would compromise “sensitive sources and methods.” For example, the C.I.A. collected other crucial information about Mihdhar that it did not provide to the F.B.I. Mihdhar, it turned out, was the son-in-law of Ahmed al-Hada, the Al Qaeda loyalist in Yemen whose phone number operated as the network’s switchboard. After arriving in New York on July 4th, Mihdhar flew to San Diego and rented an apartment. From there, he made eight calls to the Hada phone to talk to his wife, who was about to give birth. In the I-49 squad’s office, there was a link chart showing the connections between Hada’s phone and other phones around the world. Had a line been drawn from Hada’s Yemen home to Mihdhar’s San Diego apartment, Al Qaeda’s presence in America would have been glaringly obvious.

After September 11th, the C.I.A. claimed that it had divulged Mihdhar’s identity to the F.B.I. in a timely manner; indeed, both George Tenet, the agency’s director, and Cofer Black, the head of its counterterrorism division, testified to Congress that this was the case. Later, the 9/11 Commission concluded that the statements of both were false. The C.I.A. was unable to produce evidence proving that the information had been passed to the bureau.

The I-49 squad responded to the secrecy in aggressive and creative ways. When the C.I.A. refused to share intercepts of bin Laden’s satellite phone, the squad came up with a plan to build two antennae to capture the signal—one on Palau, in the Pacific, and another on Diego Garcia, in the Indian Ocean. The squad also constructed an ingenious satellite telephone booth in Kandahar, hoping to provide a convenient facility for jihadis wanting to call home. The agents could listen in on the calls, and they received videos of callers through a camera hidden in the booth. Millions of dollars and thousands of hours of labor were consumed in replicating information that other U.S. officials refused to share. According to Soufan, the I-49 agents were so used to being denied access to intelligence that they bought a CD containing the Pink Floyd song “Another Brick in the Wall.” He recalled, “Whenever we got the speech about ‘sensitive sources and methods,’ we’d just hold up the phone to the CD player and push Play.”

Just days before the June 11th meeting took place in the New York office, new threats in Yemen created a security crisis for the Americans. Yemeni authorities arrested eight men who, they said, were part of a plot to blow up the American Embassy, where Soufan and other investigators had taken refuge. Louis Freeh, the director of the F.B.I., acting on O’Neill’s recommendation, withdrew the team entirely.

By then, Soufan had a much clearer idea of the relationship between Khallad and the Cole conspirators. In July, 2001, he sent a third formal request to the C.I.A. asking for information about a possible Al Qaeda meeting in Malaysia, and about Khallad’s trip to Bangkok to meet with Quso and the Cole suicide bomber. Yet again, the agency did not respond.

On August 22nd, John O’Neill was packing boxes in his office. It was his last day at the F.B.I. He had decided to retire from the bureau after he learned of a damaging leak to the Times. The paper had reported that O’Neill’s briefcase, containing sensitive documents, was stolen while he was attending an F.B.I. conference in Florida. The briefcase was quickly recovered, and it was determined that none of the sensitive material had been touched, but it ruined his prospects at the bureau.

That day, Soufan came by O’Neill’s office to say goodbye. He was going back to Yemen later that afternoon; O’Neill’s last act as an F.B.I. agent was to sign the paperwork that would send Soufan’s team back into the country. They were determined to arrest the killers of the American sailors, despite the risks of working in such a hostile environment.

The two men walked to a nearby diner. O’Neill ordered a ham-and-cheese sandwich. “You don’t want to change your infidel ways?” Soufan kidded him, indicating the ham. “You’re gonna go to Hell.” O’Neill urged Soufan to visit him in New York when he returned. He had taken a job at the World Trade Center, as the head of security. “I’m going to be just down the road,” he said.

Soufan confided that he and his longtime girlfriend had decided to get married. O’Neill gave his blessing. “She has put up with you all this time,” he joked. “She must be a good woman.”

The week that O’Neill retired from the bureau, the F.B.I. analyst at Alec Station who had been reviewing intelligence on the Malaysia meeting realized that Mihdhar and Hazmi were in the U.S. She passed the information to Dina Corsi, at F.B.I. headquarters. Corsi, alarmed, sent an e-mail to the supervisor of the I-49 squad, ordering the unit to locate the Al Qaeda operatives. But, she added, because of the Wall no criminal investigators could be involved in the search. As it turned out, there was only one intelligence agent available, and he was new. An F.B.I. agent forwarded Corsi’s message to Steve Bongardt, Soufan’s top assistant. He called her. “Dina, you got to be kidding me!” he said. “Mihdhar is in the country?” He complained that the Wall was a bureaucratic fiction that was preventing investigators from doing their work. In a conversation the next day, he said, “If this guy is in the country, it’s not because he’s going to fucking Disneyland!” Later, he wrote in an e-mail, “Someday somebody will die—and, Wall or not, the public will not understand why we were not more effective.” The new agent’s attempt to find Mihdhar and Hazmi proved fruitless.

Three weeks later, on September 11, 2001, Soufan was at the embassy in Sanaa. He spoke on the phone with his fiancée, who told him that the Twin Towers had been attacked. He turned on a television, and watched as thesecond plane hit. He called O’Neill’s cell phone repeatedly, but there was no answer.

The F.B.I. ordered Soufan and the rest of his team in Yemen to evacuate. The morning of September 12th, the C.I.A.’s chief of station in Aden went with the agents to the airport in Sanaa. The C.I.A. official was sitting in the lounge with Soufan when he got a call on his cell phone from F.B.I. headquarters. He told Soufan, “They want to talk to you.”

Dina Corsi spoke to Soufan, and told him to stay in Yemen. He was upset. He wanted to return to New York and investigate the attack on America. “This is about that—what happened yesterday,” she told him. “Quso is our only lead.” She wouldn’t tell him any more. Soufan got his luggage off the plane, but he was puzzled. What did Quso, the Cole cameraman, have to do with September 11th?

Robert McFadden, the naval investigator, and several other officials stayed behind to help Soufan. The order from headquarters was to identify the September 11th hijackers “by any means necessary,” a directive that Soufan had never seen before. When he returned to the embassy, a fax containing photographs of twenty suspects came over a secure line. Then the C.I.A. chief drew Soufan aside and handed him a manila envelope. Inside were three surveillance photographs and a complete report about the Malaysia meeting—the very material that he had asked for so many times. The Wall had come down. When Soufan realized that the C.I.A. had known for more than a year and a half that two of the hijackers were in the country he ran into the bathroom and threw up. (Soufan’s disillusionment with the government was so profound that he eventually quit the bureau; in 2005, he became director of international operations for Giuliani Security and Safety, a company founded by Rudolph W. Giuliani, the former mayor of New York.)

Soufan went to General Qamish’s office and demanded to see Quso again. “What does this have to do with the Cole?” Qamish wanted to know. “I’m not talking about the Cole,” said Soufan. “Brother John is missing.” He started to say something else, but he was unable to continue. General Qamish’s eyes also filled with tears.

“Qamish instantly made a decision,” McFadden recalls. “He said, ‘You tell me what you want, and I’ll make it happen.’ ” Qamish said that Quso was in Aden, and there was one last flight that evening from there to the capital. He called his subordinates on the phone and began shouting, “I want Quso flown in here tonight!” Then the General called the airport and demanded to be patched through to the pilot. “You will not take off until my prisoner is aboard,” he ordered him. “You could hear them snapping to attention,” McFadden recalled.

At midnight, in a room not far from Qamish’s office, Soufan met with Quso, who was in a petulant frame of mind. “Just because something happens in New York or Washington, you don’t need to talk to me,” he said. Soufan showed him the three surveillance photographs of the Malaysia meeting, which included the Saudi hijackers Mihdhar and Hazmi. Quso thought he remembered seeing them in Al Qaeda camps, but he wasn’t certain. “Why are you asking about them?” he wanted to know.

Finally, the next day, Soufan received the fourth photograph of the Malaysia meeting—the picture of Khallad, the mastermind of the Cole operation. The two plots, Soufan instantly realized, were linked, and if the C.I.A. had not withheld information from him he likely would have drawn the connection months before September 11th. He met again with Quso, who identified the figure in the picture as Khallad—the first confirmation of Al Qaeda’s responsibility for the September 11th attacks.

Soufan interrogated Quso for three nights, while during the day he wrote reports and did research, sleeping little more than an hour at a time. “He was sick as a dog, but he was getting really good information,” his fellow-agent Carlos Fernandez recalled. On the fourth night, Soufan collapsed from exhaustion. “We wanted to medevac him out of there,” Fernandez said. “We took him to the emergency room. The kid could barely stand. But he refused to leave, and the next day he was right back at it. None of us had ever seen anything like that.” His co-workers began referring to Soufan as “an American hero.”

Soufan was intensely aware that the information he was getting was critical, and that perhaps no one else could extract the truth from Quso. Finally, after hours of extended questioning, Quso was shown a photograph of Marwan al-Shehhi, the hijacker who piloted United Airlines Flight 175, which crashed into the second tower. Quso identified him, and said that he had met Shehhi in a guesthouse in Kandahar. He remembered that Shehhi had been ill during Ramadan and that the emir of the guesthouse had taken care of him. The emir’s name was Abu Jandal.

As it happened, Abu Jandal was also in Yemeni custody, and the Americans arranged to interview him. He was a large, powerful man with a dark beard. “What are these infidels doing here?” he demanded. He took a plastic chair and turned it around, sitting with his arms crossed and his back to the interrogators. After some coaxing, Soufan got Abu Jandal to face him, but he refused to look him in the eye. Abu Jandal did want to talk, however; he delivered a lengthy, rapid-fire rant against America.

Soufan realized that the prisoner was trained in counter-interrogation techniques, since he easily agreed to things that Soufan already knew—that he had fought in Bosnia, Somalia, and Afghanistan, for instance—and denied everything else. Abu Jandal portrayed himself as a good Muslim who had considered jihad but had become disillusioned. He thought of himself not as a killer but as a revolutionary who was trying to rid the world of evil, which he believed came mainly from the United States, a country he knew practically nothing about.

As the nights passed, Abu Jandal warmed to Soufan. He told him that he was in his early thirties, older than most jihadis. He had grown up in Jeddah, Saudi Arabia—bin Laden’s home town—and he was well read in religion. He seemed to enjoy drinking tea and lecturing the Americans on the radical Islamist view of history; his sociability was a weak spot.

Soufan flattered him and engaged him in theological debate. Listening to Abu Jandal’s diatribes, Soufan picked up several useful details: that he had grown tired of fighting; that he was troubled by the fact that bin Laden had sworn loyalty to Mullah Omar, the leader of the Taliban, in Afghanistan; and that he worried about his two children, one of whom had a bone disease. Soufan also noted that Abu Jandal declined some pastries, because he was a diabetic.

The next night, the Americans brought some sugarless wafers, a courtesy that Abu Jandal acknowledged. Soufan also brought him a history of America, in Arabic. Abu Jandal was confounded by Soufan: a moderate Muslim who could argue about Islam with him, who was in the F.B.I., and who loved America. He quickly read the history that Soufan gave him and was amazed to learn of the American Revolution and its struggle against tyranny.

Soufan, meanwhile, was trying to determine the boundaries of Abu Jandal’s moral landscape. He asked him about the proper way to wage jihad. Abu Jandal eagerly talked about how a warrior should treat his adversary in battle. The Koran and other Islamic texts discuss the ethics of conduct in warfare. Where do they sanction suicide bombing? Soufan asked him. Abu Jandal said that the enemy had an advantage in weapons, but the suicide bombers evened the score. “These are our missiles,” he said. What about women and children? Soufan asked. Aren’t they supposed to be protected? Soufan pointed to the bombings of the American embassies in East Africa. He recalled a woman on a bus in front of the Nairobi embassy, who, after the bomb exploded, was found clutching her baby, trying to protect him from the flames. Both had been incinerated. What sin had the mother committed? What about the soul of her child? “God will give them their rewards in the Hereafter,” Abu Jandal said. Besides, he added, “can you imagine how many joined bin Laden after the embassy bombings? Hundreds came and asked to be martyrs.” Soufan countered that many of the East African victims—perhaps most of them—were Muslims. Several times, Abu Jandal quoted clerical authorities or chapters from the Koran, but he found that Soufan was more than a match for him on theological matters. Abu Jandal finally asserted that, because the embassy bombings were on a Friday, when the victims should have been in the mosque, they were not real Muslims.

On the fifth night, Soufan slammed a news magazine on the table between them. The magazine had photographs of the airplanes crashing into the Twin Towers—graphic shots of people trapped in the buildings and jumping a hundred stories. “Bin Laden did this,” Soufan told him. Abu Jandal had heard about the attacks, but he didn’t know many details. He studied the pictures in amazement. He said that they looked like a “Hollywood production,” but the scale of the atrocity visibly shook him.

Soufan and Abu Jandal were joined in the small interrogation room by McFadden and two Yemeni investigators. Everyone sensed that Soufan was closing in. American and allied troops were preparing to go to war in Afghanistan, but they desperately needed more information about the structure of Al Qaeda, the locations of hideouts, and the plans for escape—all of which American intelligence officials hoped Abu Jandal could supply.

Coincidentally, a local Yemeni paper was on a shelf under the coffee table. Soufan showed it to Abu Jandal. The headline read, “TWO HUNDRED YEMENI SOULS PERISH IN NEW YORK ATTACK.” (At the time, the death-toll estimates were in the tens of thousands.) Abu Jandal read the headline and drew a breath. “God help us,” he muttered. Soufan asked what kind of Muslim would do such a thing. Abu Jandal insisted that the Israelis must have committed the attacks on New York and Washington. “The Sheikh is not that crazy,” he said of bin Laden.

Soufan then took out a book of mug shots containing photographs of known Al Qaeda members and of the hijackers. He asked Abu Jandal to identify them. The Yemeni flipped through them quickly and closed the book.

Soufan opened the book again and told him to take his time. “Some of them I have in custody,” he said, hoping that Abu Jandal wouldn’t realize that the hijackers were all dead. Abu Jandal paused for a half-second on the photograph of Shehhi, the pilot of United Airlines Flight 175, before he started to turn the page. “You’re not done with this one,” Soufan said. “Ramadan, 1999. He’s sick. You’re his emir, and you take care of him.” Abu Jandal looked at Soufan in shock. “When I ask you a question, I already know the answer,” said Soufan. “If you’re smart, you’ll tell me the truth.”

Abu Jandal conceded that he knew Shehhi and gave his Al Qaeda nom de guerre, Abdullah al-Sharqi. He did the same with Khaled al-Mihdhar and five others, including Mohammed Atta, the lead hijacker. But he still insisted that bin Laden would never commit such an action. It was the Israelis, he maintained.

“I know for sure that the people who did this were Al Qaeda guys,” said Soufan. He took seven photographs out of the book and laid them on the table.

“How do you know?” Abu Jandal asked. “Who told you?”

“You did,” said Soufan. “These are the hijackers. You just identified them.”

Abu Jandal turned pale. He covered his face with his hands. “Give me a moment,” he pleaded. Soufan walked out of the room. When he came back, he asked Abu Jandal what he thought now. “I think the Sheikh went crazy,” he said. And then he told Soufan everything he knew. ♦